Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

nu_correct not found
by Bernardo jose 15 Nov '13

15 Nov '13

Hello experts, Could you please help me? I have already checked perl is in usr/bin/perl. Sincerely, Bernardo. nu_correct.mni.log is: tmpdir is ./tmp.mri_nu_correct.mni.2629 /Users/bernardomartins/Desktop/manoel/manoel/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2629/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2629/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=4.18, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2629/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Nov 15 14:23:57 BRST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.2629/nu0.mnc ./tmp.mri_nu_correct.mni.2629/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2629/0/ -iterations 1000 -distance 50 nu_correct: Command not found. ERROR: nu_correct

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Re Freesurfer type
by Anna Jonsson 15 Nov '13

15 Nov '13

Dear list members, I was wondering where in the Freesurfer output the information on which freesurfer version has been used to process scans is located? eg recon-all.log? Thank you, Kind Wishes, Anna

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freesurfer5.3 version In CentOS5
by Rujing Zha 15 Nov '13

15 Nov '13

Dear all, In CentOS5,which freesurfer5.3 version(centos4 or centos6?) can be compatible? Thanks! All the best. 2013-11-15 Rujing Zha

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are there any previous studies on the robustness of freesurfer default parameters as used in cortical thickness computation?
by Mark Alexiuk 15 Nov '13

15 Nov '13

Hi, My interest is in cortical thickness measurements for longitudinal Alzheimer data, namely the ADNI dataset. My understanding is that recon-all can be used to generate cortical thicknesses. I am trying to understand how the default parameter values used in recon-all were arrived at. Are the default parameters optimized in some sense? How robust are the default parameters with respect to the resulting cortical thickness? Will a small change in a parameter value result in a significant difference in some cortical thicknesses? I was able to find the following and would appreciate references to good papers on this topic. Excerpt from abstract: Standard manual tracing and FreeSurfer-based analyses were performed in 77 participants including 67 cognitively normal individuals and 10 individuals with early Alzheimer's disease.... The manual and FreeSurfer approaches yielded nearly identical estimates of amyloid burden (intraclass correlation = 0.98) as assessed by the mean cortical binding potential. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0073377 Thanks for any forthcoming comments. Mark

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list of FreeSurfer 5.3 labels
by Del Re, Elisabetta 15 Nov '13

15 Nov '13

Hi, I am trying to find a list of all the labels available for FreeSurfer 5.3 and am having a hard time finding it. Any suggestions? Thank you, regards, Elisabetta del Re

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Generation of brodmann area label and statistics..
by Gonzalo Rojas Costa 15 Nov '13

15 Nov '13

Hi: I have some freesurfer processed studies.... I used 5.1 version, and now I found that it don't has the brodmann area labels and statistics generated in some studies... How can I create it without doing again the complete recon-all ?.... Sincerely, -------------------------------- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Newest freeview version...
by Gonzalo Rojas Costa 15 Nov '13

15 Nov '13

Hi: Which is the freeview newest version ?... the one that is included in freesurfer 5.3.0 package ?... Sincerely, Gonzalo Rojas Costa -------------------------------- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Re: [Freesurfer] Is transformation matrix in .nii (nifti) header applied by FS?
by Douglas N Greve 14 Nov '13

14 Nov '13

you will see some differences due to reslicing and interpolation. These differences should be somewhat random, so they might be difficult to detect in a group analysis. But in general, you should treat all your data the same. On 11/14/2013 03:40 PM, cabe(a)uos.de wrote: > thanks, that was already helpful. > > But does the fact that the transformation is carried out affect the results? > I mean, the images has to be resliced and interpolated during this > transformation. So intensities change slightly. If i would process the > same subject, once with and once without an reorientation in the beginning > as start input data, would you expect a difference? > > Or in other words, if you would compare groups, where one group was AC-PC > aligned with SPM before freesurfer processing and the other was not, could > any of the differences be attributed to the different input files > (transformation matrix in the nii header). > > Chris > >> There are two matrices in the nifti file (qform and sform). By default >> we use the qform. The qform is 6 dof and so is probably not appropriate >> for your talairach transform. Bottom line is that the sform is probably >> being ignored. >> >> doug >> >> >> On 11/14/2013 07:18 AM, cabe(a)uos.de wrote: >>> Hello, >>> >>> I have a question regarding nifti (.nii) input files. I have .nii image >>> files, which are aligned to AC-PC with SPM. The actual (original) data >>> in >>> this file is not changed, but the transformation matrix is saved in the >>> .nii file. >>> >>> When displaying the freesurfer reconstructed results with tkmedit, the >>> images are tilted (AC-PC aligned). So it seems that freesurfer reads and >>> applies the transformation saved in the nii file. >>> >>> Is that true? and if yes at which step? >>> >>> When using the recon-all -i command to create the starting folders and >>> mgz >>> files before starting the actual freesurfer processing, is the >>> transformation matrix used to realign the images during this first >>> process, and the following processing is done on the reoriented image? >>> or >>> is it just used for display? Or is the fact that the image appears >>> tilted >>> a result of the Talairach transform and the nii header was not read at >>> all? >>> >>> I am asking because, I have subjects which were SPM aligned, and subject >>> which were not. I am wondering if it makes any difference, since due to >>> an >>> initial reorientation data will be interpolated and maybe a bit >>> smoothed, >>> compared to data which was not aligned before. >>> >>> Does anybody have any experience with that and a feeling if an >>> reorientation beforehand would have an effect on the outcome for >>> cortical >>> thickness maesures? >>> >>> Thaks for any comments, >>> Chris >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Seg fault with mri_segstats?
by Douglas N Greve 14 Nov '13

14 Nov '13

Hmmm, I can't replicate this error. This is 5.3 I assume? doug On 11/12/2013 06:02 PM, Michael Waskom wrote: > sorry, unclear why the original email wasn't included in the reply. > copied here: > > > I'm running into a strange seg fault when trying to use mri_segstats > (it's actually ocurring within mri_glmfit-sim, but I can reproduce it > manually) > > This is the line that fails (stripping the leading paths for readability): > > mri_segstats --seg cache.th20.pos.sig.ocn.mgh --exclude 0 --i > concat_output.nii.gz --sum mri_glmfit-sim.junk.84357 --avgwf > cache.th20.pos.y.ocn.dat > > With the log: > > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ > cwd > cmdline mri_segstats --seg > /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/osgm/cache.th20.pos.sig.ocn.mgh > --exclude 0 --i > /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/concat_output.nii.gz > --sum mri_glmfit-sim.junk.84357 --avgwf cache.th20.pos.y.ocn.dat > sysname Darwin > hostname ben-octocore.stanford.edu <http://ben-octocore.stanford.edu/> > machine i386 > user mwaskom > UseRobust 0 > Loading > /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/osgm/cache.th20.pos.sig.ocn.mgh > Loading > /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/concat_output.nii.gz > Voxel Volume is 1 mm^3 > Generating list of segmentation ids > Found 5 segmentations > Computing statistics for each segmentation > 1 1 10934 10934.000 > 2 2 2409 2409.000 > 3 3 1620 1620.000 > 4 4 2044 2044.000 > > Reporting on 4 segmentations > Computing spatial average of each frame > 0 1 2 3Segmentation fault > > > Intriguingly, it does not segfault if I remove the --avgwf parameter > OR the --exclude 0 parameter. It does segfault if I use --avgwfvol > instead of --avgwf > > I'm not too sure what's going on, I can otherwise read the > segmentation file and --y file and do statistical operations on them, > and I can write other files to the directory I'm testing this in. > > Here's my system info: > > FREESURFER_HOME: /usr/local/freesurfer/5.3.0 > > Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 > > Kernel info: Darwin 10.8.0 i386 > > Any thoughts? > > > On Tue, Nov 12, 2013 at 1:36 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > sorry, what is this in response to? > > > > On 11/06/2013 08:13 PM, Michael Waskom wrote: > > Hi Doug, > > I can't discern anything off about these images, but I hope > it's easy to figure out! They can be downloaded from here ; I > figured that was easiest. > > Michael > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Is transformation matrix in .nii (nifti) header applied by FS?
by cabe＠uos.de 14 Nov '13

14 Nov '13

Hello, I have a question regarding nifti (.nii) input files. I have .nii image files, which are aligned to AC-PC with SPM. The actual (original) data in this file is not changed, but the transformation matrix is saved in the .nii file. When displaying the freesurfer reconstructed results with tkmedit, the images are tilted (AC-PC aligned). So it seems that freesurfer reads and applies the transformation saved in the nii file. Is that true? and if yes at which step? When using the recon-all -i command to create the starting folders and mgz files before starting the actual freesurfer processing, is the transformation matrix used to realign the images during this first process, and the following processing is done on the reoriented image? or is it just used for display? Or is the fact that the image appears tilted a result of the Talairach transform and the nii header was not read at all? I am asking because, I have subjects which were SPM aligned, and subject which were not. I am wondering if it makes any difference, since due to an initial reorientation data will be interpolated and maybe a bit smoothed, compared to data which was not aligned before. Does anybody have any experience with that and a feeling if an reorientation beforehand would have an effect on the outcome for cortical thickness maesures? Thaks for any comments, Chris

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Freesurfer November 2013